Looking good! 👍
I don't know if you've read Rohwer's "Coral Reefs in the Microbial Seas" but this negative feedback loop you've described with algae and coral is central to his DDAM model of reef degradation. Something disrupts corals or the primary herbivores are lost and algae is able to take over by out competing corals and dumping bad types of DOC into the water which further stress corals. All those sponges you have help stabilize the ecosystem by removing all types of labile DOC much faster than anything else can. (Sponges remove in 20-30 minutes what bacteria take 3 weeks to remove.) And water changes are still the only way to remove the refractory DOC in our systems.

It might be a growth or a rock/shell stuck in it gill or maybe a large parasitic isopod. Only way to know for sure is going to be catch it, hold it gently in a wet towel (aquarium water) and examine it.

Congratulations on training your flasher wrasse! Are you going to do a training video? Do you use voice or visual commands or both?
My guess on the sponge is it's one of the Haliclona species tube sponge

No, you didn't misunderstand me. I maintain the first two systems in my post with just tapwater and dechlorinator (Austin has pretty decent tapwater). No RO or RO/DI filter is used. (No skimmer, dosers, reactors or refugiums either.) New saltwater is made up at the time of water change and allowed to sit however long it takes to siphon out some water.

When calculating the life expectancy of the GAC filter cartridges it's best to periodicly measure the actual ratio of "waste water" to filtrate. Not all RO membranes are the same and water pressure can vary by a surprising amount so the amount of rejected water to filtered water can be much higher than 3:1.
In my maintenance business I use 3 stage RO, 5 stage RO/DI and just plain tapwater treated with dechlorinator (Ammo Detox) and haven't seen any difference. When troubleshooting reef problems old filters are often pointed to as a cause and they may be if they are letting chlorine get into the system but in my experience maintaining systems with tapwater I would look someplace else for the problem. Here's the two systems I've been maintaining with tapwater treated with dechlorinator:
And here's a system maintained with a water softener then GAC filters (no dechlorinator):

Yes clams reproduce sexually. some species have separate sexes, some are hermaphrodites and some are sequential hermaphrodites. I haven't been able to verify the exact species I have in my tanks but my suspicion is they are hermaphrodites. Tridacna clams are sequential hermaphrodites starting off male and switching to females.

Yup, that's what hapens with blue/green chromis. IMO they should only be left to experienced aquarists. A colorful combination of hardy damsels would be a Talboti, Azure, Rolland's and a Yellow Belly. All four are Chrysiptera species, have the same body size and shape and same behavior. They are similar enough they will set up thier own hierarchy and from what I've I wouldn't be surprised to see mating behavior.

For starters I would recommend Forrest Rohwer's "Coral Reefs in the Microbial Seas". It's an excellent introduction to Dissolved Organic Carbon (DOC) and points out whether the equilibrium promotes algae or corals is independent of nutrients. In my two nuisance algae threads on this forum being patient and using only manual removal nuisance algae disappeared as inorganic nutrients increased.
This system is one I think demonstrates the idea that it's the equilibrium that matters and not the amount of nitrate or PO4 per se that matters. Being maintained now for roughly 8 years with tapwater the "gurus" say can't be done.
And I have to disagree with the idea sunlight causes nuisance algae problems. The different spectrum may be a challenge for the average hobbyist to know how to stock and deal with initially but the simple techniques I posted in my two algae threads work just as well if sunlight is a source of light. Here's my system that gets seasonal variable of 1\2 to 2 1\2 hours:

Viperspectra or Mars Aqua are a couple options. Kessils, from what I've seen the last few years, have roughly a 10% failure rate at the 3 year mark but they use glass lenses which won't discolor over time like polycarbonate lenses will.

I wouldn't use it while cycling. once a system is mature you might use it if you're feeding a lot and PO4 is climping above .5 mg/l. Keep in mind PO4 defciency can really screw up phototrophs (animals with zooxanthellae).